Mock community taxonomic profiling benchmark (Portik et al. 2022)
Eleven profiling methods (14 configurations) on PacBio HiFi, ONT and Illumina reads from ATCC and ZymoBIOMICS mock communities, scored on species detection and abundance.
No reviewed evaluations are linked here in this release. See the sources and separately identified configurations below.
Overview
Eleven profiling methods (14 configurations) on PacBio HiFi, ONT and Illumina reads from ATCC and ZymoBIOMICS mock communities, scored on species detection and abundance.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Published results still to collect
This release has no source-checked evaluations linked to this page. It does not mean that the benchmark has no published results.
Charts will appear when compatible result tables have been checked against their sources.
Results
All evaluations
0 evaluations · 0 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
No evaluations linked in this release.
Source checking is not independent reproduction. Release 2026-10-09-8cc1db47c7f9.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 12 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
Baseline status by linked protocol
- HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) · 0/2 roles measured
- HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) · 0/2 roles measured
- Illumina ATCC MSA-1003 mock community (HiSeq 2500): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) · 0/2 roles measured
- Illumina ZymoBIOMICS D6300 standard (NovaSeq 6000), subsampled: species detection at 0.001% of total reads (Portik et al. 2022 Table 4) · 0/2 roles measured
- ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) · 0/2 roles measured
- ONT R10.3 ZymoBIOMICS D6300 standard, length-filtered (GridION): species detection at 0.001% of total reads (Portik et al. 2022 Table 4) · 0/2 roles measured
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-09-8cc1db47c7f9. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this benchmark. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Evidence
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Evidence table
Inspect claims, sources and review details
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Sources and history
Release 2026-10-09-8cc1db47c7f9 · Record review: source checked
1 source records and release history
- Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets · Original source · BMC Bioinformatics 23:541, published 2022-12-13; PMC9749362 full-text XML
Technical metadata and extraction receipts
Stable ID: dna-pathogen-20261009-benchmark-portik2022-mock-communities
- areas
- microbes-communities
- contexts
- clinical_research
- entity level
- suite
- version
- BMC Bioinformatics 2022, Table 4
- task
- Species-level presence detection and relative abundance estimation in mock microbial communities
- source locator
- Tables 1-4; Methods 'Detection metrics' and 'Relative abundance estimates'
- scope note
- Genus-level and higher-threshold results (Additional file 1 Tables S10-S16) and the shorter-read and simulated short-read variants are not extracted.
- limitations
- Mock communities of cultured organisms without human host DNA; not clinical specimens.; Reference databases differ between methods (Table 2), so method and database effects are confounded.
Related records
- part of: HiFi ATCC MSA-1003 mock community (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4)
- part of: HiFi ZymoBIOMICS D6331 gut microbiome standard (PacBio Sequel II HiFi): species detection at 0.001% of total reads (Portik et al. 2022 Table 4)
- part of: Illumina ATCC MSA-1003 mock community (HiSeq 2500): species detection at 0.001% of total reads (Portik et al. 2022 Table 4)
- part of: Illumina ZymoBIOMICS D6300 standard (NovaSeq 6000), subsampled: species detection at 0.001% of total reads (Portik et al. 2022 Table 4)
- part of: ONT Q20 ZymoBIOMICS D6300 standard, length-filtered (PromethION): species detection at 0.001% of total reads (Portik et al. 2022 Table 4)
- part of: ONT R10.3 ZymoBIOMICS D6300 standard, length-filtered (GridION): species detection at 0.001% of total reads (Portik et al. 2022 Table 4)